The genome assembly of the koala is reported in a paper published online in Nature Genetics. This high quality genome represents the most complete genome sequence for a marsupial to date. The data give insight into the highly specialized koala diet, consisting of eucalyptus leaves, and provide information that may be useful to combatting infectious disease. Read more
The sea lamprey (Petromyzon marinus) is an important model in evolutionary biology. It was discovered in 2009 (http://www.pnas.org/content/106/27/11212.long) that the genome of the sea lamprey undergoes extensive programmed genome rearrangement during development, where ~0.5 Gb (around 20%) of DNA is eliminated from the genome. The somatic tissues contain smaller genomes and only the germ cells retain the full complement of genetic material. The genome of the sea lamprey had been sequenced previously from the blood and liver, so only the somatic genome has been thoroughly characterized (https://www.nature.com/articles/ng.2568). Read more
Continuing with our month-long celebration of Nature Genetics 25th anniversary, I have chosen to highlight a study by Sarah Fortune and colleagues estimating mutation rate differences between different lineages of Mycobacterium tuberculosis published in June 2013. Read more
A new study published online this week in Nature Genetics reports the discovery of novel host targets of HIV infection identified from a high-throughput CRISPR/Cas9-based screen. This screen was performed in CD4 + T-cells and was designed to find candidate genes required for successful HIV infection, but whose inactivation did not affect cell viability. In this way, potential drug targets for anti-HIV therapy could be discovered. Read more
Protein degradation is a highly coordinated process with multiple levels of regulation, including both targeted and autodegradation. This sophisticated cascade of protein turnover must be precisely balanced to maintain proper physiological function. A recent article published in Nature Genetics reports the discovery of gene with protein-truncating mutations that lead to the skin condition epidermolysis bullosa, which is characterized by tendency to blister, itching and other abnormalities. The authors found 5 patients all with start codon mutations in the KLHL24 gene, which encodes Kelch-like protein 24, a substrate receptor of the cullin 3 (CUL3)–RBX1–KLHL24 ubiquitin ligase complex. Read more
Rice is one of the most important crops on the planet, responsible for feeding billions of people. Given this global significance, studying rice in different geographies can be useful and aid in harnessing genetic diversity underlying particular traits and adaptations favorable to different environments. African rice (Oryza glaberrima Steud.) is mainly grown in sub-Saharan Africa and known for its stress tolerance. In a new article this week in Nature Genetics, Michael Purugannan and colleagues report the whole genome re-sequencing of 93 African rice landraces from various regions of Western coastal and sub-Saharan Africa. They create a genome-wide SNP map and through comparative genomic analysis study the domestication and population history of African rice. They use their map to perform GWAS for salt tolerance and find 11 significantly associated regions, highlighting the value of this unique genetic resource. Read more
The trajectory of tumor cells during metastasis can be influenced by many factors, including the physical environment and the genetic makeup of metastatic clones. In high-grade serous ovarian cancer, there are limited barriers in the intraperitoneal space, allowing for extensive spreading and mixing of tumor cells. A recent article published in Nature Genetics explores these different patterns of clonal evolution in metastatic ovarian cancer using a combination of bulk and single cell sequencing. Read more
A high-quality assembly of the carrot (Daucus carota) genome is reported this week in Nature Genetics. Carrot is an important crop due to its high content of Vitamin A precursors, alpha- and beta-carotenes, as well as its popularity in global cuisines. The bright orange color of the modern carrot and its high carotenoid content are features that emerged through selection and breeding- the complete genome sequence will serve as a resource to aid breeders in crop improvement strategies. Read more
Type 1 and Type 2 diabetes (T1D and T2D) are complex diseases characterized by insulin signaling defects resulting from either autoimmune deregulation or metabolic dysfunction, respectively. Both cause disruption of blood glucose regulation and can lead to significant systemic effects. Despite the physiological distinctions underlying disease development, there are commonalities between T1D and T2D; in T1D, pancreatic beta cells are targeted by the autoimmune system, while in T2D there is gradual, progressive beta cell mass decline. There are some shared genetic risk factors associated with both conditions, but distinguishing between genetic versus secondary causes related to beta cell failure has been challenging. Read more
Antibiotics emerged as miracle drugs and “silver bullets” in the early 20th century, revolutionizing medicine and our ability to combat infectious disease while positively impacting health and lifespans on a large scale. This remarkable triumph held steady for many years, and consequently antibiotic research and development diminished as a priority due to the seeming defeat of bacterial infections. However, the selective pressure that came with antibiotic exposure led to the development of bacterial resistance to these compounds, motivating renewed interest in what is now an extremely important public health issue. Mechanisms of resistance are many and ever-evolving, and we know now that it is not a matter of IF bacteria will become resistant to a class of antibiotics, but when. The search for new and potentially exploitable bacterial vulnerabilities, then, becomes a constant enterprise in order for us to keep pace with the bacteria in the antibiotics/resistance arms race. Read more
